18-1916607-A-G

Variant names:

• chr18-1916607-A-G
• rs9949006
• ENST00000584867.1:n.197-9961T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000584867.1(ENSG00000263745):​n.197-9961T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (28810 hom., cov: 19)
• Consequence: ENSG00000263745 ENST00000584867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484
• Publications: 5 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584867.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000263745	ENST00000584867.1	TSL:2	n.197-9961T>C		intron	N/A
	ENSG00000266602	ENST00000653094.1		n.527-39980A>G		intron	N/A
	ENSG00000266602	ENST00000653330.1		n.452+44676A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.640 AC: 88426 AN: 138134 Hom.: 28780 Cov.: 19

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.594

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.663

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.640 AC: 88486 AN: 138206 Hom.: 28810 Cov.: 19 AF XY: 0.640 AC XY: 42575 AN XY: 66514

African (AFR) AF: 0.698 AC: 25478 AN: 36502

American (AMR) AF: 0.723 AC: 9414 AN: 13026

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2127 AN: 3410

East Asian (EAS) AF: 0.671 AC: 3167 AN: 4718

South Asian (SAS) AF: 0.669 AC: 2989 AN: 4466

European-Finnish (FIN) AF: 0.557 AC: 4656 AN: 8354

Middle Eastern (MID) AF: 0.566 AC: 154 AN: 272

European-Non Finnish (NFE) AF: 0.597 AC: 38610 AN: 64700

Other (OTH) AF: 0.667 AC: 1255 AN: 1882

Alfa AF: 0.612 Hom.: 40452

Bravo AF: 0.658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.59
PhyloP100		0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9949006;

hg19: chr18-1916608;